[Biojava-l] Finding Annotation keys for parsed reports and inconsistent Blast parsing errors...

[Matthew Pocock]

DeAngelo Lampkin wrote:
> Is there some place that lists all the keys that are stored in Annotations for various types of reports that are parsed (specifically BLAST in my case)? Or are we stuck with manually going in,? 
> listing them all and "seeing before trying".  Say it ain't so! :)  

At the moment there isn't anything describing these annotations. This is 
what the AnnotationType objects are for. The next push from me for the 
1.4 series is to add AnnotationType schemas to things like this, and 
have static AnnotationType instances emitted into the javadoc as 
human-readable text.

Somebody else will have to help you with your blast error, though - 
would you belive I don't parse that many blasts?

Matthew

> 
> Also, I've been getting inconsistent errors when parsing Blast reports. Specifically, I get an error when I try parsing a BLAST report using the BlastParser program given in Biojava in Anger (nice title BTW) while the Blast2HTML parser in the demos directory (also using the BlastLikeSaxParser) runs perfectly fine.  So the problem is probably actually in the ContentHandler or the SeqSimilarityAdapter.  Anyway, the error that the BlastParser program returns is:
> 
> -----------------------------
> "org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.6 is not supported by the biojava blast-like parsing framework
>         at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:241)
>         at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160)
>         at BlastParser.main(BlastParser.java:43)"
> -------------------------
> 
> Any help is greatly appreciated!
> 
> Thanks,
> 
> DeAngelo Lampkin
> Scientific Programmer
> Xencor
> 626 - 737 - 8083
> 
> 
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